Posted
by
samzenpus
on Thursday March 07, 2013 @07:27PM
from the new-germ-on-the-block dept.

tverbeek writes "Russian scientists believe they have found a new type of bacteria in the sub-glacial Lake Vostok. From the article: 'The samples obtained from the underground lake in May 2012 contained a bacteria which bore no resemblance to existing types, said Sergei Bulat of the genetics laboratory at the Saint Petersburg Institute of Nuclear Physics.
"After putting aside all possible elements of contamination, DNA was found that did not coincide with any of the well-known types in the global database," he said. "We are calling this life form unclassified and unidentified," he added.'"

That's hyperbole, I'm afraid. It's a bacterium, just a very distant cousin. Great for studying evolution, irrelevant to Michael Chrichton. Based on the other bacteria recovered from the borehole sample, its hobbies most likely consist of "feeding on geothermal heat" and "being adapted to an extremely stable, homogeneous environment with no predators or other forms of life," which as a general rule means it's as helpless as the Kakapo [wikipedia.org].

I understand the rationale behind the general rule as stated, but is it totally impossible that a strain of this could survive even an extreme change in environment, adapt and thrive to such a degree that it would become a danger to the natives of that environment?

I mean, I know it's more extreme than, say, eucalyptus trees in California or rabbits in Australia, but to write off the possibility completely seems like an exaggerated response.

Based on circumstantial evidence (another species found nearby), the bacterium is a thermophile that depends on geothermal heat for warmth. Because of the way thermophiles evolve, it is pretty much certain that the proteins in this species are non-functional at colder temperatures; the samples collected were either dead or in a deep state of antifreeze-clogged hibernation.

It's also 700 million years (or more!) behind on immune defences, which means it's vulnerable to everything from the toxins that all plants constantly secret all the time to the macrophages in our blood. The immune game is a Red Queen scenario [wikipedia.org]—either a pathogen is at the forefront of innovation, or it's susceptible to the most basic form of detection.

The only environment this could possibly intrude upon is one comparable to its own—maybe a heat vent in another frozen lake. Even if it wasn't a thermophile, it would be dead meat on the surface because of bacteriophages (viruses). To add insult to injury, as far as we know this bacterium has no competitors and is not part of a community, making it highly unlikely that it has any competition or any defences.

Gene retention is like lactose tolerance—if you don't use it, you'll lose it. For animals, this typically takes a few thousand years. For bacteria it happens much more quickly. They're very simple organisms, and they're very good at adapting, but only if they've had time to adjust to their new setting. In this case, every single one of its (probably several thousand) genes has spent millions of years being fine-tuned for the most boring environment possible. It has absolutely no hope.

Uhm, where did you get that figure? 700 million years is two supercontinent cycles [wikipedia.org] ago - Antarctica was slightly north of the equator then. The antarctic ice cap didn't even start to form until the end of the Eocene. According to wikipedia, lake Vostok [wikipedia.org] may have been isolated for the past 15 to 25 million years.

If you scrutinize the article, Sergei Bulat is quoted as saying the organism has less than 86% "DNA similarity" to other species. Taken at face value, this means that the entire genome of the bacterium is less than 86% similar, which (a) requires isolating it first and months of work, and (b) would not be impressive at all, since Escherichia coli genomes have much higher variety.

He then goes on to say that 90% is the threshold beyond which a species is considered completely unknown. This is an appropriate figure to give when discussing the evolution of one particular gene called the 16S ribosomal RNA, which is very important to cellular function and changes very slowly. It's also a standard test to use in the analysis of bacterial communities, and one of the core tools in metagenomics, because it's very unique to species and hence an excellent fingerprint. If you need citations to back up this claim, I can give you oceans of them. This is my actual day job.

So how divergent is 100 – 86 = 14%? This article [pnas.org] references a standard 1% every 50 million years. 14 * 50 = 700 million years. This figure is quite possibly too low in this case, since evolution has a non-linear effect on sequences—eventually mutations flip multiple times, and so large numbers of changes get masked. This rate of change can be sped to 2% every 50 million years if the environment is exceptionally rich and predator-free, like inside certain cells in insects—but that's largely because the host cell is available to a degree to provide nutrients, so proper ribosomal function isn't as important.

This doesn't mean necessarily that this species has been completely isolated the whole time, just that we haven't found any surviving links. If it previously existed in a cave system, for example, that entire community could have been wiped out when Antarctica froze, leaving behind only a stub of organisms that were sheltered by the heat (and food chain) emanating from the thermal vent. Cave ecosystems often contain numerous species that have adapted so tightly to their niche that they are unable to survive outside.

That being said, this expedition has already made crap up for publicity stunts [guardian.co.uk]. As this hasn't been published in any journals yet and was instead released to the press first, it's entirely possible that no such species exists. Nevertheless, the claim of 14% divergence will be interpreted by other experts as more than half a billion years.

If not phages then something else. Protists. Nematodes. If it's really been isolated for this long, it probably has a really slow doubling time; that may be bad enough that predation could overwhelm it.

That being said, though, evolutionary pressure is still key. Viruses are host-specific because the hosts keep changing; an older bacterium is more likely to have exploitable sugar moieties on its surface.

Viruses decide what to stick to by looking for unique features on the outsides of cells. Bacteria are more or less all the same on the inside, so once it's in, it's in. Phages have their own reproductive machinery for the most part; they just need a cell to reside in. One of the unique features they can stick to are glycoproteins and glycolipids embedded in the exterior cell wall (a second phospholipid bilayer that surrounds the membrane). To be honest it's fairly likely that these evolve so quickly that no

You mean 1,000,000,000 years ago? That's when multicellular life was prolific, after a couple of billion years being much simpler.You do know Antarctica was part of the super-continent the dinosaurs inhabited eh? Its also only been frozen for around 25 million years too.

Yyyyeah, well... if it was only isolated from the rest of the biological tree for 25 million years, we'd only see about 0.5-1% difference in the 16S rRNA. TFA reported (what I think) is at least 14% difference, which is at least 700 million years. Either all of its relatives died off, or it's been down there at that thermal vent this whole time, only vaguely aware (in an "evolutionary pressures" kinda sense) of the ice around it.

Very possible—in which case they either also function as time capsules from various points in history, or they're close enough to a circulating system that there's nothing interesting. I'm sure the people working on this project expected to find something that dated to the last freeze.

>That's hyperbole, I'm afraid. It's a bacterium, just a very distant cousin.

I know. Which is still very cool. Sometimes you just want it to be something extra, extra cool; like a bacterium-like organism that got there from some ancient Martian meteorite and thrived there. Even better would be some spawn of Cthulhu that escaped the Mountains of Madness and hid beneath the ice. Me, I keep looking for a fossil bryophyte with a branching sporophyte.

Archaeans and obligate parasites are as close as it gets. Archaeans are ancient and only found in bizarre environments (like acid mines, where the pH is below zero) because they were driven out by their more successful offspring, vowing one day to retake the crown and reclaim Earth for themselves. (Not really, but it sounds good.) Obligate parasites like Cryptosporidium have wildly strange genomes, spending millions of years festering in the flesh of others, finding new ways to ditch seemingly-vital functio

I don't think it's published yet. TFA mentions "less than" 86% DNA "similarity", which I think was supposed to be 86% 16S RNA homology, in which case, the bacterium has been separated from the nearest known species for at least 700 million years.

I don't know how this stuff works so can only stupidly speculate that it will be interesting to try to follow the mutations this wee beastie underwent to let it survive in its current home, and that it somehow could be interesting if not useful when comparing that to some of its closer cousins on our side of the lake.

Might there be clues that let us make more robust some of our helpful bacteria? Or even clues to help combat some of the 'super-bugs' that are really scary in their resistance to anti-biotics,

There's a good chance it has some neat antifreeze proteins. It's most likely very vulnerable to antibiotics, though; biological war far is an arms race. We can only learn from analysing the enemy and things similar to it.

But your homework is not going to dissappear, it will just become URGENT.

Take a break and get cracking!

I'm over 50, but still trying to complete a degree on telematics in the next year, so I know; homework sucks but if you don't get your nose in the grinder, it doesn't get done. Even if you know more about the subject that your professors, you still need to turn in good homework or they'll fail you.

Russians are the first to start confirming reports that there is new DNA that is not our own on this planet....they chose to bring it forth this way, but will eventually lead to actual confirmation of life from outer space and that they have arrived/landed....probably through a ship at the bottom of the lake.

Or I might have just finished watching x files marathon...take your pick.

Actually, there's a pretty good chance it'll die off before then. It's been isolated for at least half a million years (possibly a lot longer), and their drill bit was contaminated with at least sixteen species of other bacteria. You get the picture—entropy, genies, bottles, et cetera.

I'm not exactly sure if this invalidates your comment, but Uranus is not believed to have a distinct surface underneath its atmosphere. The most popular model suggests that it just gets denser and denser, culminating in a rapidly-spinning mantle-ocean of water, ammonia, and other gasses long before the actual rocky core.